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- PDB-3lie: Crystal Structure of the extracellular domain of the putative his... -

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Basic information

Entry
Database: PDB / ID: 3lie
TitleCrystal Structure of the extracellular domain of the putative histidine kinase vpHK1S-Z8
ComponentsPutative sensory box/GGDEF family protein
KeywordsSIGNALING PROTEIN / PDC fold
Function / homology
Function and homology information


diguanylate cyclase / protein histidine kinase activity
Similarity search - Function
: / Bacterial histidine kinase, sensor domain / Periplasmic sensor-like domain superfamily / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. ...: / Bacterial histidine kinase, sensor domain / Periplasmic sensor-like domain superfamily / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. / PAS domain / Nucleotide cyclase / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 Å
AuthorsZhang, Z. / Hendrickson, W.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural characterization of the predominant family of histidine kinase sensor domains.
Authors: Zhang, Z. / Hendrickson, W.A.
History
DepositionJan 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative sensory box/GGDEF family protein
B: Putative sensory box/GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5604
Polymers68,5112
Non-polymers492
Water54030
1
A: Putative sensory box/GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2802
Polymers34,2551
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative sensory box/GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2802
Polymers34,2551
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.049, 114.953, 69.624
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B8 - 274
2111A8 - 274

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Components

#1: Protein Putative sensory box/GGDEF family protein


Mass: 34255.449 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 28-313)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP0354 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87SR8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 2M NaCl, 0.2M MgCl, 0.1M Tris, pH 7.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97921 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 19533 / % possible obs: 97.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.077 / Χ2: 0.989 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.694.10.35518820.72895.9
2.69-2.84.10.28518730.8596.2
2.8-2.9340.21318971.03496.7
2.93-3.0840.15219221.07497.1
3.08-3.2840.11819291.08797.4
3.28-3.5340.09219481.05598.8
3.53-3.884.20.07319901.08599.4
3.88-4.454.50.06119841.01699.4
4.45-5.64.60.05720200.92398.9
5.6-504.80.07220881.02697.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.59 Å39.02 Å
Translation2.59 Å39.02 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→39.028 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.444 / SU ML: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.189 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.326 991 5.1 %RANDOM
Rwork0.254 ---
obs0.258 19501 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.66 Å2 / Biso mean: 57.454 Å2 / Biso min: 19.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.59→39.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4285 0 2 30 4317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224348
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9585895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2685523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81224.358218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.97815749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0481527
X-RAY DIFFRACTIONr_chiral_restr0.1030.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213321
X-RAY DIFFRACTIONr_mcbond_it0.7241.52632
X-RAY DIFFRACTIONr_mcangle_it1.35924251
X-RAY DIFFRACTIONr_scbond_it1.83131716
X-RAY DIFFRACTIONr_scangle_it3.0224.51644
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 2092 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.10.05
TIGHT THERMAL0.160.5
LS refinement shellResolution: 2.592→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 76 -
Rwork0.322 1222 -
all-1298 -
obs--90.08 %

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